/**
* Add a optional column which has stable order and name, into {@link #optionalColumnMapping} and
* {@link #columnMapping}.
*
* @see MZTabColumn#createOptionalColumn(Section, MZTabColumn, Integer, IndexedElement)
* @exception IllegalArgumentException: If user would like to add duplicate optional columns.
* @param column SHOULD NOT set null.
* @param msRun SHOULD NOT set null.
*/
public void addOptionalColumn(MZTabColumn column, MsRun msRun) {
String position = column.getLogicPosition();
if (optionalColumnMapping.containsKey(position)) {
throw new IllegalArgumentException(
"There exists column "
+ optionalColumnMapping.get(position)
+ " in position "
+ position);
}
MZTabColumn newColumn = null;
// switch (section) {
// case Protein_Header:
// if (column.getName().equals(ProteinColumn.NUM_PSMS.getName()) ||
// column.getName().equals(ProteinColumn.NUM_PEPTIDES_DISTINCT.getName())
// ||
// column.getName().equals(ProteinColumn.NUM_PEPTIDES_UNIQUE.getName()))
// {
// newColumn = MZTabColumn.createOptionalColumn(section, column, msRun);
// }
//
// if (position.equals(ProteinColumn.SEARCH_ENGINE_SCORE.getOrder()) ||
// position.equals(ProteinColumn.NUM_PSMS.getOrder()) ||
// position.equals(ProteinColumn.NUM_PEPTIDES_DISTINCT.getOrder()) ||
// position.equals(ProteinColumn.NUM_PEPTIDES_UNIQUE.getOrder())) {
// newColumn = MZTabColumn.createOptionalColumn(section, column, msRun);
// }
// break;
// case Peptide_Header:
// if (position.equals(PeptideColumn.SEARCH_ENGINE_SCORE.getOrder())) {
// newColumn = MZTabColumn.createOptionalColumn(section, column, msRun);
// }
// break;
// case Small_Molecule_Header:
// if (position.equals(SmallMoleculeColumn.SEARCH_ENGINE_SCORE.getOrder())) {
// newColumn = MZTabColumn.createOptionalColumn(section, column, msRun);
// }
// break;
// }
if (section == Section.Protein_Header) {
if (column.getName().equals(ProteinColumn.NUM_PSMS.getName())
|| column.getName().equals(ProteinColumn.NUM_PEPTIDES_DISTINCT.getName())
|| column.getName().equals(ProteinColumn.NUM_PEPTIDES_UNIQUE.getName())) {
newColumn = MZTabColumn.createOptionalColumn(section, column, null, msRun);
}
}
if (newColumn != null) {
optionalColumnMapping.put(newColumn.getLogicPosition(), newColumn);
columnMapping.put(newColumn.getLogicPosition(), newColumn);
}
}
/**
* Judge the column is optional or not, based one its header name.
*
* @param header SHOULD NOT be null!
*/
public boolean isOptionalColumn(String header) {
header = header.trim().toLowerCase();
switch (section) {
case Protein_Header:
if (header.startsWith(ProteinColumn.SEARCH_ENGINE_SCORE.getName())
|| header.startsWith(ProteinColumn.NUM_PSMS.getName())
|| header.startsWith(ProteinColumn.NUM_PEPTIDES_DISTINCT.getName())
|| header.startsWith(ProteinColumn.NUM_PEPTIDES_UNIQUE.getName())
|| header.startsWith("protein_abundance_assay")
|| header.startsWith("protein_abundance_study_variable")
|| header.startsWith("protein_abundance_stdev_study_variable")
|| header.startsWith("protein_abundance_std_error_study_variable")) {
return true;
}
break;
case Peptide_Header:
if (header.startsWith(PeptideColumn.SEARCH_ENGINE_SCORE.getName())
|| header.startsWith("peptide_abundance_assay")
|| header.startsWith("peptide_abundance_study_variable")
|| header.startsWith("peptide_abundance_stdev_study_variable")
|| header.startsWith("peptide_abundance_std_error_study_variable")) {
return true;
}
break;
case Small_Molecule_Header:
if (header.startsWith(SmallMoleculeColumn.SEARCH_ENGINE_SCORE.getName())
|| header.startsWith("smallmolecule_abundance_assay")
|| header.startsWith("smallmolecule_abundance_study_variable")
|| header.startsWith("smallmolecule_abundance_stdev_study_variable")
|| header.startsWith("smallmolecule_abundance_std_error_study_variable")) {
return true;
}
break;
}
return header.startsWith("opt_");
}